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BBGProtocols
BBGProtocols
- BBGlab best practices on data organization
- Info for bbg-coffee drinkers
Cluster basics
Cluster basics
- Backups
- Headers
- Interactive
- New folder in workspace
- Running notebooks in the cluster
- Screen
- Structure
- Queues
- Terminal
- Submitting jobs
  Submitting jobs
  - Qmap Submit
  - SLURM
Datasets
Datasets
- BBG standards
  BBG standards
  - Variant consequences
- General datasets
  General datasets
  - BeatAML
  - CGCI
  - CPTAC
  - GENIE
  - Hartwig
  - ICGC
  - Oncotree Repository
  - PCAWG
  - PedcBioPortal
  - St. Jude
  - St. Jude LIFE
  - TARGET
  - TCGA
  - UK Biobank
  - cBioPortal
- Inhouse datasets
  Inhouse datasets
- Other data
  Other data
IRB
IRB
- VPN
- Eduroam
- Fifteen wifi
Methods
Methods
- Sequencing
  Sequencing
  - Bedtools
  - Bowtie2
  - Cutadapt
  - Fastqc
  - SAMtools
  - Trimmomatic Trimmomatic
    Table of contents
    
    Description
    
    Reference
  - Vep
  - pysam
  - Variant callers
    Variant callers
    
    HMFtools
    
    MosaicForecast
    
    Mutect2
    
    Platinum
    
    Sarek
  - singleCell
    singleCell
    
    ArchR: Processing scATAC sequencing data
    
    CellRanger
    
    Mosaic - python package
    
    Seurat
    
    Tapestri insights
    
    Tapestri pipeline
- Signature
  Signature
Plots and scripts
Plots and scripts
Tools
Tools
- Conda
- Docker
- GitHub Copilot
- McGyver
- Nextflow
- Snakemake
- BBG tools
  BBG tools
  - BGconfig
  - BGdata
  - BGlogs
  - BGpack
  - BgReference
  - BGsignature
  - BGvep
  - OpenVariant
- Programming
  Programming
  - Git
  - Python
    Python
    
    Updating package on pypi
- Singularity
  Singularity
- VSCode
  VSCode
  - VSCode from the bbg-cluster
  - VSCode in interactive node

Table of contents

Description
Reference

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